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Within the promoters and enhancers of NF-\u03baB-responsive genes, we identified clusters of non-consensus \u03baB DNA sites, many exhibiting low affinity for NF-\u03baB in vitro. Deletion of these sites demonstrated their collective critical role in transcription. We explored how these \u201cweak\u201d \u03baB sites exert their influence, especially given the typically low nuclear concentrations of NF-\u03baB. Using proteomics approaches, we identified additional nuclear factors, including other DNA-binding TFs, that could interact with \u03baB site-bound NF-\u03baB RelA. ChIP-seq and RNA-seq analyses suggest that these accessory TFs, referred to as the TF-cofactors of NF-\u03baB, facilitate dynamic recruitment of NF-\u03baB to the clustered weak \u03baB sites. Overall, the occupancy of NF-\u03baB at promoters and enhancers appears to be defined by a collective contribution from all \u03baB sites, both weak and strong, in association with specific cofactors. This congregation of multiple factors within dynamic transcriptional complexes is likely a common feature of transcriptional programs.<\/jats:p>","DOI":"10.1093\/nar\/gkaf846","type":"journal-article","created":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T02:57:15Z","timestamp":1759978635000},"source":"Crossref","is-referenced-by-count":0,"title":["Teamwork of clustered low-affinity \u03baB sites and accessory factors regulates transcriptional strength of NF-\u03baB RelA dimers"],"prefix":"10.1093","volume":"53","author":[{"given":"Shandy","family":"Shahabi","sequence":"first","affiliation":[{"name":"University of California San Diego Department of Chemistry and Biochemistry, , 9500 Gilman Drive , La Jolla, CA 92093 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tapan","family":"Biswas","sequence":"additional","affiliation":[{"name":"University of California San Diego Department of Chemistry and Biochemistry, , 9500 Gilman Drive , La 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